Genomic analysis of tRNA gene sets

Abstract

Methods for identifying one or more positions of conserved difference in a set of similar sequence strings are provided, as well as systems and devices for identifying one or more positions of conserved difference in a set of similar sequence strings, and sets of positions of conserved differences.

What is claimed is:  
     
         1 . A method for identifying one or more positions of conserved difference in a set of similar sequence strings, the method comprising: 
 providing a set of similar sequence strings derived from a plurality of species, wherein each similar sequence string comprises at least n sequence elements;    comparing the at least n sequence elements in a first similar sequence string to the at least n sequence elements in a second similar sequence string, for a first species of the plurality of species;    assigning a value to each of n positions of the at least n sequence elements, based upon whether the sequence elements are identical or different in the two similar sequence strings;    repeating the comparing and assigning for each species in the plurality of species;    summing the values assigned for each of the n positions across the plurality of species; and    identifying which of the n positions have the greatest sum value, thereby identifying the positions of conserved difference in the set of similar sequence strings.    
     
     
         2 . The method of  claim 1 , wherein each species in the plurality of species contributes at least two similar sequence strings to the set of similar sequence strings.  
     
     
         3 . The method of  claim 1 , wherein each species in the plurality of species contributes more than two similar sequence strings to the set of similar sequence strings.  
     
     
         4 . The method of  claim 1 , wherein the providing a set of similar sequence strings comprises: 
 providing a set of sequences;    providing logical instructions for recognizing a target sequence string; and    using the logical instructions to analyze the sequences and identify the target sequence strings, thereby providing a set of similar sequence strings.    
     
     
         5 . The method of  claim 1 , wherein the set of similar sequence strings comprises sets of amino acid sequences, nucleic acid sequences, lipid-based sequences or carbohydrate sequences.  
     
     
         6 . The method of  claim 5 , wherein the set of similar sequence strings comprises a set of tRNA molecules.  
     
     
         7 . The method of  claim 5 , wherein the set of similar sequence strings comprises a set of alleles.  
     
     
         8 . The method of  claim 7 , wherein the set of alleles comprises at least two alleles.  
     
     
         9 . The method of  claim 7 , wherein the set of alleles comprises more than two alleles.  
     
     
         10 . The method of  claim 1 , wherein the plurality of species comprises a plurality of prokaryotic species, eukaryote species, or combinations thereof.  
     
     
         11 . The method of  claim 8 , wherein the plurality of prokaryotic species comprises a plurality of eubacteria species, archaea species, or combinations thereof.  
     
     
         12 . The method of  claim 1 , wherein the comparing and assigning is performed in a computer.  
     
     
         13 . The method of  claim 1 , further comprising determining whether the positions that have the greatest sum values comprise elements which interact with a protein, a peptide, a protein complex, a nucleic acid, a protein-nucleic acid complex, a carbohydrate chain, or a combination thereof.  
     
     
         14 . The method of  claim 13 , wherein the protein comprises an enzyme.  
     
     
         15 . The method of  claim 13 , wherein the protein-nucleic acid complex comprises a ribosome.  
     
     
         16 . The method of  claim 1 , further comprising determining whether the positions that have the greatest sum values comprise modified elements.  
     
     
         17 . The method of  claim 16 , wherein the modified elements comprise amino acids or nucleotides which are modified by methylation, acetylation, ubiquitination, lysinylation or glycosylation.  
     
     
         18 . A method for identifying one or more positions of conserved difference in a set of similar sequence strings, the method comprising: 
 providing a set of similar sequence strings derived from a plurality of species, wherein each similar sequence string comprises at least n sequence elements, and wherein each species in the plurality of species contributes two or more similar sequence strings to the set of similar sequence strings;    simultaneously comparing the at least n sequence elements for the two or more similar sequence strings from a first species of the plurality of species;    assigning a value to each of n positions of the at least n sequence elements, based upon whether the sequence elements are identical or different in the two or more similar sequence strings;    repeating the comparing and assigning for each species in the plurality of species;    summing the values assigned for each of the n positions across the plurality of species; and    identifying which of the n positions have the greatest sum value, thereby identifying the positions of conserved difference in the set of similar sequence strings.    
     
     
         19 . The set of conserved differences in a set of similar sequence strings as identified by the method of  claim 1 .  
     
     
         20 . A computer or computer-readable medium comprising one or more logical instructions for identifying at least one conserved difference in a set of similar sequence strings derived from a plurality of species, 
 wherein each species in the plurality of species comprises at least two similar sequence strings; and    wherein the logical instructions compare at least n sequence elements in a first similar sequence string to at least n sequence elements in a second similar sequence string, for a first species of the plurality of species; assigns a value to each of n positions of the at least n sequence elements, based upon whether the sequence elements are identical or different in the two similar sequence strings; repeats the comparing and assigning for each species in the plurality of species; sums the values assigned for each of the n positions across the plurality of species; and identifies which of the n positions have the greatest sum value, thereby identifying the positions of conserved difference in the set of similar sequence strings.    
     
     
         21 . The computer or computer-readable medium of  claim 20 , further comprising a database comprising the set of similar sequence strings derived from a plurality of species.  
     
     
         22 . The computer or computer-readable medium of  claim 20 , comprising a neural network.  
     
     
         23 . The computer or computer-readable medium of  claim 20 , comprising a user interface.  
     
     
         24 . The computer or computer-readable medium of  claim 23 , wherein the user interface comprises an input field that permits data entry of the similar sequence strings.  
     
     
         25 . The computer or computer-readable medium of  claim 23 , wherein the user interface comprises a data output file.  
     
     
         26 . The computer or computer-readable medium of  claim 23 , wherein the user interface operates across a network.  
     
     
         27 . The computer or computer-readable medium of  claim 23 , wherein the user interface operates across the internet.  
     
     
         28 . The computer or computer-readable medium of  claim 23 , wherein the user interface comprises a web browser interface.